Related papers: Finite-temperature local protein sequence alignmen…
In context of laser powder bed fusion (L-PBF), it is known that the properties of the final fabricated product highly depend on the temperature distribution and its gradient over the manufacturing plate. In this paper, we propose a novel…
The packing of elastic sheets is investigated in a quasi two-dimensional experimental setup: a sheet is pulled through a rigid hole acting as a container, so that its configuration is mostly prescribed by the cross-section of the sheet in…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Self-consistency improves reasoning by aggregating diverse stochastic samples, yet the dynamics behind its efficacy remain underexplored. We reframe self-consistency as a dynamic distributional alignment problem, revealing that decoding…
We consider a high-dimensional random constrained optimization problem in which a set of binary variables is subjected to a linear system of equations. The cost function is a simple linear cost, measuring the Hamming distance with respect…
At zero temperature coupled cluster theory is widely used to predict total energies, ground state expectation values and even excited states for molecules and extended systems. Generalizations to finite temperature exist, however, they are…
We propose a free-energy-perturbation approach accelerated by machine-learning potentials to efficiently compute transition temperatures and entropies for all rungs of Jacob's ladder. We apply the approach to the dynamically stabilized…
In deep learning-based classification tasks, the softmax function's temperature parameter $T$ critically influences the output distribution and overall performance. This study presents a novel theoretical insight that the optimal…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure…
We investigate the normal mode spectrum of a trapped ion chain at the symmetry-breaking linear to zigzag transition and at finite temperatures. For this purpose we modulate the amplitude of the Doppler cooling laser in order to excite and…
We show that an high temperature expansion at fixed order parameter can be derived for the quantum Ising model. The basic point is to consider a statistical generating functional associated to the local spin state. The probability at…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
Temperature of a finite-sized system fluctuates due to the thermal fluctuations. However, a systematic mathematical framework for measuring or estimating the temperature is still underdeveloped. Here, we incorporate the estimation theory in…
We study the fluctuations of the directed polymer in 1+1 dimensions in a Gaussian random environment with a finite correlation length {\xi} and at finite temperature. We address the correspondence between the geometrical transverse…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
We study the correlation functions of quantum spin $1/2$ ladders at finite temperature, under a magnetic field, in the gapless phase at various relevant temperatures $T\neq 0$, momentum $q$ and frequencies $\omega$. We compute those…
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
Free energy differences are a central quantity of interest in physics, chemistry, and biology. We develop design principles that improve the precision and accuracy of free energy estimators, which has potential applications to screening for…